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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctagaaatatcccaaactctattctctgattaacaaaaacccattacccaccagcatgagcattcgttgacatttgatcctcatccgatgattgcgcagGTGACAGAGAACGGGAAGCAGGAGCGGCATCTAGTGGCCACGGTGGGGAAGTACAGCGTGGTGTGGAACTTCTTGCAGGTGAAGAACAGCCACCACGAGT

Basic information

species Zea mays
transcript GRMZM2G131638_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G131638_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g08190.1 (Oryza sativa), 3'ss of exon 1
--gctagaaa--tatcccaaactctattctctgattaacaaaaacccattacccaccagcatgagcattcgttgacatttgatcctcatccgatgattgcgcagGTGACAGAGAACGGGAAGCAGGAGCGGCATCTAGTGGCCACGGTGGGGAAGTACAGCGTGGTGTGGAACTTCTTGCAGGTGAAGAACAGCCACCACGAGT
   ||||||    |   |  |  |  ||   |  ||          |||  ||  | | |   |  |||| |     | |||   |  |  |  |   | | ||||||| |||||||||||||||||| ||||||| ||||| ||||||||||||||||||||||||||||||||| | |||||||||||||||||||||||||
aaactagaatacaaatgctgatgcgtttacatcgttggttttgttgcat--cctgcaaacccaaaaattcat--gtttgtgaatgtgctgtgtgggcggtgtagGTGACCGAGAACGGGAAGCAGGAGAGGCATCTGGTGGCGACGGTGGGGAAGTACAGCGTGGTGTGGAACTTCCTCCAGGTGAAGAACAGCCACCACGAGT

upper sequence: GRMZM2G131638_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G04290.1 (Glycine max), 3'ss of exon 1
----gctagaaatatcccaaactctattctctgat-taacaaaaacccattacccaccagcatgagcattcgttgacatttgatcctcatccgatgattgcgcagGTGACAGAGAACGGGAAGCAGGAGCGGCATCTAGTGGCCACGGTGGGGAAGTACAGCGTGGTGTGGAACTTCTTGCAGGTGAAGAACAGCCACCACGAGT
    ||| || | ||  || |   |  | | |  | |  |    |    |||  ||  || |     |||  |  |  |   |   | ||    || |  |  ||||||||||||| ||||| |||||||| ||| |||| ||||| |||||||||| ||| ||| | |||||||||   || || ||| |  |    || ||||
gtctgct-gagaaatgacatatcttggtttttactgtgtctttcatattttaatcataaggaaatatatttttataattccaagttttat----tggtgtcttagGTGACAGAGAATGGGAAACAGGAGCGACATATAGTAGCCACCGTGGGGAAGTTCAGTGTGATATGGAACTTCCAACAAGTCAAGGATGGTTCTCATGAGT

upper sequence: GRMZM2G131638_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA04G04120.1 (Glycine max), 3'ss of exon 1
gctagaaatatcccaaactctattctctgattaacaaaaacccattacccaccag-catgagcattcgttgacatttgatcctcatccgatgattgcgcagGTGACAGAGAACGGGAAGCAGGAGCGGCATCTAGTGGCCACGGTGGGGAAGTACAGCGTGGTGTGGAACTTCTTGCAGGTGAAGAACAGCCACCACGAGT
 | | |  |      || |    |||  | ||         |  | |      |  |||| | |    |     | | || |  |     ||  |||  ||||||||||||| ||||| |||||||||||| |||| ||||| |||||||||| ||| ||| | |||||||||   || || ||| |  |    || ||||
-ccacatctgctgagaaatgacatcttggtttttattgtgtctttcatattttaatcatgtggaaatatatttttattattccaacttcttggatgcttagGTGACAGAGAATGGGAAACAGGAGCGGCATATAGTAGCCACTGTGGGGAAGTTCAGTGTGATATGGAACTTCCAACAAGTCAAGGATGGTTCTCATGAGT

upper sequence: GRMZM2G131638_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv03s0063g00480.t01 (Vitis vinifera), 3'ss of exon 1
---gctagaaatatcccaaactctattctctgattaacaaaaacccattacccaccagcatgagcattcgttgacat-ttgatcctcatccgatgattgcgcagGTGACAGAGAACGGGAAGCAGGAGCGGCATCTAGTGGCCACGGTGGGGAAGTACAGCGTGGTGTGGAACTTCTTGCAGGTGAAGAACAGCCACCACGAGT
     |   | |   | ||  |  | | |  || ||      |   |  |   |  ||||   | | |  | ||  | |||    | ||    |  || |  ||||||| ||||| ||||| || |||||||||||||| || || ||||| |||| ||||||| | |||||||||  ||||||||| |||||    || ||||
ttcagttccagtcgtcaaagataaactattggactactcgtcaa--aaaaaaaaaaagcaattggactgatggatgtgttgcattttatattgtatttcc--agGTGACTGAGAATGGGAAACAAGAGCGGCATCTAGTTGCAACAGTGGGCAAGTTCAGCGTGATATGGAACTTCCAGCAGGTGAAAAACAGTAGTCATGAGT

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|60398831|gb|DN231647.1|DN231647
EST:     CTCATCTAGCAGGAGCAAACAGCAGGTTCAGGGAGGGCAGATTCTCATGG                         GTGACAGAGAACGGGAAGCAGGAGCGGCATCTAGTGGCCACGGTGGGGAAG
genomic: CTCATCTAGCAGGAGCAAACAGCAGGTTCAGGGAGGGCAGATTCTCATGGgtgagtatat ... gattgcgcagGTGACAGAGAACGGGAAGCAGGAGCGGCATCTAGTGGCCACGGTGGGGAAG
EST: gi|87157830|gb|DY402619.1|DY402619
EST:     CTCATCTAGCAGGAGCAAACAGCAGGTTCAGGGAGGGAAGATTCTCATGG                         GTGACGGAGAACGGGAAGCAGGAGCGGCATCTAGTGGCCACGGTGGGGAAG
genomic: CTCATCTAGCAGGAGCAAACAGCAGGTTCAGGGAGGGCAGATTCTCATGGgtgagtatat ... gattgcgcagGTGACAGAGAACGGGAAGCAGGAGCGGCATCTAGTGGCCACGGTGGGGAAG
EST: gi|76930314|gb|DV172334.1|DV172334
EST:     CTCATCTAGCAGGAGCAAACAGCAGGTTCAGGGAGGGCAGATTCTCATGG                         GTGACAGAGAACGGGAAGCAGGAGCGGCATCTAGTGGCCACGGTGGGGAAG
genomic: CTCATCTAGCAGGAGCAAACAGCAGGTTCAGGGAGGGCAGATTCTCATGGgtgagtatat ... gattgcgcagGTGACAGAGAACGGGAAGCAGGAGCGGCATCTAGTGGCCACGGTGGGGAAG
EST: gi|71760947|gb|DR958884.1|DR958884
EST:     CTCATCTAGCAGGAGCAAACAGCAGGTTCAGGGAGGGCAGATTCTCATGG                         GTGACAGAGAACGGGAAGCAGGAGCGGCATCTAGTGGCCACGGTGGGGAAG
genomic: CTCATCTAGCAGGAGCAAACAGCAGGTTCAGGGAGGGCAGATTCTCATGGgtgagtatat ... gattgcgcagGTGACAGAGAACGGGAAGCAGGAGCGGCATCTAGTGGCCACGGTGGGGAAG
EST: gi|26559454|gb|CA831689.1|CA831689
EST:     CTCATCTAGCAGGAGCAAACAGCAGGTTCAGGGAGGGAAGATTCTCATGG                         GTGACGGAGAACGGGAAGCAGGAGCGGCATCTAAGTGGCCACGGTGGGGAA
genomic: CTCATCTAGCAGGAGCAAACAGCAGGTTCAGGGAGGGCAGATTCTCATGGgtgagtatat ... gattgcgcagGTGACAGAGAACGGGAAGCAGGAGCGGCATCTA-GTGGCCACGGTGGGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacccaccagcatgagcattcgttgacatttgatcctcatccgatgattgcgcagGTGACAGAGAACGGGAAGCAGGAGCGGCATCTAGTGGCCACGGTGGGGAAGTACAGCGTGGTGTGGAACTTCTTGCAGGTGAAGAACAGCCACCACGAGT
                           atttgat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctagaaatatcccaaactctattctctgattaacaaaaacccattacccaccagcatgagcattcgttgacatttgatcctcatccgatgattgcgcagGTGACAGAGAACGGGAAGCAGGAGCGGCATCTAGTGGCCACGGTGGGGAAGTACAGCGTGGTGTGGAACTTCTTGCAGGTGAAGAACAGCCACCACGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - aacaaaa
- - - - - - - - - - - - - - - - - - - - - - - - -caccagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agcattc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgacatt